Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGGTTGCTGGTTTTGCAATCTACTCGCTTATGTATGACCGTCATAAAAGCTGGTATTCCTGGATTTTGGGATCTTTGACAAGTTGTGTGTATACATTTGgtaagttcaaggccatcattggtgattattcatgtttttctgggtgcacttgttggcttctctggatatcaattcaagtaattggttattagacagtcacacgtcgttaatggtggttatgtcgagtactaacctgttcatatgtaccag

Basic information

species Physcomitrella patens
transcript PP1S64_201V6.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S64_201V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA06G16940.1 (Glycine max), 5'ss of exon 10
TTGGTTGCTGGTTTTGCAATCTACTCGCTTATGTATGACCGTCATAAAAGCTGGTATTCCTGGATTTTGGGATCTTTGACAAGTTGTGTGTATACATTTGgtaagttcaaggccatcattggtgattattcatgtttttctgggtgc--acttgttggcttctctggatatcaattcaagt-aattggttattagacagtcacacgtcgttaatggtggttatgtcgagtactaacctgttcatatgtaccag
 | |||||||||||| |  | |||||||| |||||||| ||||| || ||||||||||| |||||| ||   ||  | ||||||||||| || |  |||||||||  |    |     |  |  || |||  ||||||| | | | |   | | |    |  |    | | | ||  ||||  |||    |||| |||   |                                                   
CTTGTTGCTGGTTTTTCTGTTTACTCGCTGATGTATGAGCGTCACAAGAGCTGGTATTCTTGGATTCTGTCTTCGCTCACAAGTTGTGTATACATGTTTGgtaagcactcttcttggttatgctatgatt-gtgtttttgttgatactaccatataaaatcatgaccacaactatctaagttgattaa--attaaacaaaaat--------------------------------------------------
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|37828146|gb|BJ586158.1|BJ586158
EST:     CTGGTATTCCTGGATTTTGGGATCTTTGACAAGTTGTGTGTATACATTTG                         GTTTTATCATGATGTGTCCACAGCTTTTTATCAACTACAAGTTGAAGTCTG
genomic: CTGGTATTCCTGGATTTTGGGATCTTTGACAAGTTGTGTGTATACATTTGgtaagttcaa ... tatgtaccagGTTTTATCATGATGTGTCCACAGCTTTTTATCAACTACAAGTTGAAGTCTG
EST: gi|67727249|gb|BJ977508.1|BJ977508
EST:     GACAAGTTGTGTGTATACATTTTG                         GTTTTATCATGATGTGTCCACAGCTTTTTATCAACTACAAGTTGAAGTCT
genomic: GACAAGTTGTGTGTATACA-TTTGgtaagttcaa ... tatgtaccagGTTTTATCATGATGTGTCCACAGCTTTTTATCAACTACAAGTTGAAGTCT
EST: gi|208365740|gb|DC944168.1|DC944168
EST:     CTGGTATTCCTGGATTTTGGGATCTTTGACAAGTTGTGTGTATACATTTG                         GTTTTATCATGATGTGTCCACAGCTTTTTATCAACTACAAGTTGAAGTCTG
genomic: CTGGTATTCCTGGATTTTGGGATCTTTGACAAGTTGTGTGTATACATTTGgtaagttcaa ... tatgtaccagGTTTTATCATGATGTGTCCACAGCTTTTTATCAACTACAAGTTGAAGTCTG
EST: gi|162178561|gb|FC355013.1|FC355013
EST:     CTGGTATTCCTGGATTTTGGGATCTTTGACAAGTTGTGTGTATACATTTG                         GTTTTATCATGATGTGTCCACAGCTTTTTATCAACTACAAGTTGAAGTCTG
genomic: CTGGTATTCCTGGATTTTGGGATCTTTGACAAGTTGTGTGTATACATTTGgtaagttcaa ... tatgtaccagGTTTTATCATGATGTGTCCACAGCTTTTTATCAACTACAAGTTGAAGTCTG
EST: gi|162210480|gb|FC386776.1|FC386776
EST:     CTGGTATTCCTGGATTTTGGGATCTTTGACAAGTTGTGTGTATACATTTG                         GTTTTATCATGATGTGTCCACAGCTTTTTATCAACTACAAGTTGAAGTCTG
genomic: CTGGTATTCCTGGATTTTGGGATCTTTGACAAGTTGTGTGTATACATTTGgtaagttcaa ... tatgtaccagGTTTTATCATGATGTGTCCACAGCTTTTTATCAACTACAAGTTGAAGTCTG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 31 (upstream exon), 33 (downstream exon)
Score: 2

TTGGTTGCTGGTTTTGCAATCTACTCGCTTATGTATGACCGTCATAAAAGCTGGTATTCCTGGATTTTGGGATCTTTGACAAGTTGTGTGTATACATTTGgtaagttcaa ... tatgtaccagGTTTTATCATGATGTGTCCACAGCTTTTTATCAACTACAAGTTGAAGTCTGTAGCTCACATGCCTTGGCGACAGATGACCTACAAGTTCCTCAATACTAT




<











<


<